ADL: PBS script for virtual screening

Amor A. San Juan amorasj at bii.a-star.edu.sg
Fri Jan 18 01:31:52 PST 2008


Hi everyone,

I need help in writing a PBS script to submit to linux cluster. I am stuck
and need your assistance so greatly, as I dont have enough programming
skills.

I already generated all the rest of input files for executable autodock,
such as *dpf, gridmaps etc. Now I need simple PBS script to submit to
cluster.

Below is the default PBS script, which I dont have precise idea on how to
put some arguments prior submitting to cluster.

#!/bin/sh
#PBS -l arch=x86_64
#PBS -q MP
#PBS -l nodes=4:ppn=4:smp
#PBS -l ncpus=4
#PBS -l walltime=00:05:00
#PBS -l mem=100mb
#PBS -V
#PBS -m bea
#PBS -o Output_File
#PBS -e Error_File
cd $PBS_O_WORKDIR
mpirun -np 4 -machinefile $PBS_NODEFILE ./a.out
~

Would someone please explain in detail or send a file of  the  PBS script
submitted to cluster?

Thanks
Amor





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